Chapter 10 Spirochaetota
10.1 MCI
GIFTs_functions_community %>%
rowMeans() %>%
as_tibble(., rownames = "sample") %>%
left_join(sample_metadata, by = join_by(sample == sample)) %>%
# filter(time_point=="0_Wild") %>%
group_by(diet) %>%
summarise(MCI = mean(value), sd = sd(value)) %>%
tt()| diet | MCI | sd |
|---|---|---|
| Post_grass | 0.2396430 | 0.01304278 |
| Pre_grass | 0.2493529 | 0.01524032 |
| Wild | 0.2541861 | 0.02059163 |
MCI <- GIFTs_functions_community %>%
rowMeans() %>%
as_tibble(., rownames = "sample") %>%
left_join(sample_metadata, by = join_by(sample == sample))
# %>%
# filter(diet!="Post_grass")
shapiro.test(MCI$value)
Shapiro-Wilk normality test
data: MCI$value
W = 0.98397, p-value = 0.8693 Df Sum Sq Mean Sq F value Pr(>F)
diet 2 0.001317 0.0006583 2.39 0.107
Residuals 33 0.009090 0.0002755 
10.4 Wilcoxon comparison
10.4.1 Community elements differences:
| Elements | Pre_grass | Wild | Function | Element | Difference | group_color |
|---|---|---|---|---|---|---|
| D0702 | 2.176967e-01 | 4.215706e-01 | Alcohol degradation_Ethanol | Ethanol | -0.2038739000 | Wild |
| D0708 | 6.562387e-02 | 1.137517e-01 | Alcohol degradation_Phytol | Phytol | -0.0481278300 | Wild |
| D0705 | 2.174659e-01 | 2.932360e-01 | Alcohol degradation_Propylene glycol | Propylene glycol | -0.0757701000 | Wild |
| D0509 | 3.498560e-01 | 4.690221e-01 | Amino acid degradation_Arginine | Arginine | -0.1191661000 | Wild |
| D0505 | 2.884142e-01 | 3.728710e-01 | Amino acid degradation_Valine | Valine | -0.0844568000 | Wild |
| B0307 | 2.568247e-01 | 3.888024e-01 | Amino acid derivative biosynthesis_Spermidine | Spermidine | -0.1319777000 | Wild |
| D0903 | 1.047526e-03 | 2.363183e-03 | Antibiotic degradation_Cephalosporin | Cephalosporin | -0.0013156570 | Wild |
| D0904 | 3.904555e-05 | 1.422616e-03 | Antibiotic degradation_Oxacillin | Oxacillin | -0.0013835705 | Wild |
| B0902 | 9.761388e-06 | 3.556539e-04 | Metallophore biosynthesis_Aerobactin | Aerobactin | -0.0003458925 | Wild |
| D0608 | 3.360954e-04 | 1.404321e-02 | Nitrogen compound degradation_Betaine | Betaine | -0.0137071121 | Wild |
| D0306 | 2.292213e-01 | 3.300262e-01 | Sugar degradation_D-Xylose | D-Xylose | -0.1008049000 | Wild |
| D0806 | 2.616052e-05 | 9.531525e-04 | Xenobiotic degradation_Anthranilate | Anthranilate | -0.0009269920 | Wild |
| D0811 | 3.527381e-06 | 1.281851e-04 | Xenobiotic degradation_Benzoyl-CoA | Benzoyl-CoA | -0.0001246577 | Wild |
| D0808 | 1.952277e-06 | 7.113078e-05 | Xenobiotic degradation_Cumate | Cumate | -0.0000691785 | Wild |
| D0819 | 4.314553e-05 | 1.892106e-03 | Xenobiotic degradation_Mercury | Mercury | -0.0018489605 | Wild |
